title: Effective classification of microRNA precursors using feature mining and AdaBoost algorithms.
abstract: MicroRNAs play important roles in most biological processes, including cell proliferation, tissue differentiation, and embryonic development, among others. They originate from precursor transcripts (pre-miRNAs), which contain phylogenetically conserved stem-loop structures. An important bioinformatics problem is to distinguish the pre-miRNAs from pseudo pre-miRNAs that have similar stem-loop structures. We present here a novel method for tackling this bioinformatics problem. Our method, named MirID, accepts an RNA sequence as input, and classifies the RNA sequence either as positive (i.e., a real pre-miRNA) or as negative (i.e., a pseudo pre-miRNA). MirID employs a feature mining algorithm for finding combinations of features suitable for building pre-miRNA classification models. These models are implemented using support vector machines, which are combined to construct a classifier ensemble. The accuracy of the classifier ensemble is further enhanced by the utilization of an AdaBoost algorithm. When compared with two closely related tools on twelve species analyzed with these tools, MirID outperforms the existing tools on the majority of the twelve species. MirID was also tested on nine additional species, and the results showed high accuracies on the nine species. The MirID web server is fully operational and freely accessible at http://bioinformatics.njit.edu/MirID/ . Potential applications of this software in genomics and medicine are also discussed.
authors.affiliation: Bioinformatics Program and Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey 07102, USA.
authors.forename: Ling
authors.initials: L
authors.lastname: Zhong
authors.forename: Jason T L
authors.initials: JT
authors.lastname: Wang
authors.forename: Dongrong
authors.initials: D
authors.lastname: Wen
authors.forename: Virginie
authors.initials: V
authors.lastname: Aris
authors.forename: Patricia
authors.initials: P
authors.lastname: Soteropoulos
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Shapiro
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods; D057225:Data Mining / Q000379:methods; D030561:Databases, Nucleic Acid; D006801:Humans; D020407:Internet; D035683:MicroRNAs / Q000737:chemistry / Q000145:classification* / Q000235:genetics; D012322:RNA Precursors / Q000737:chemistry / Q000145:classification* / Q000235:genetics; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012984:Software
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors